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Structural Basis of Biological Function > Protein Structure Revision > Flashcards

Protein Structure Revision Flashcards

1
Q

What is the function and give an example of a Structural Protein ?

A
  • Provide structural components

- Collagen and Keratin

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2
Q

What is the function and give an example of a Contractile Protein ?

A
  • Move muscles

- Myosin and Actin

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3
Q

What is the function and give an example of a Transport Protein ?

A
  • Carry essential substances throughout the body

- Haemoglobin and Lipoprotein

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4
Q

What is the function and give an example of a Storage Protein ?

A
  • Store nutrients

- Casein and Ferritin

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5
Q

What is the function and give an example of a Hormone Protein ?

A
  • Regulate body metabolism and nervous system

- Insulin and Growth Hormone

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6
Q

What is the function and give an example of an Enzyme Protein ?

A
  • Catalyse biochemical reactions in the cells

- Sucrase and Trypsin

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7
Q

What is the function and give an example of a Protection Protein ?

A
  • Recognise and destroy foreign substances

- Immunoglobulins

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8
Q

What is meant by a Homomultier and Heteromultimer ?

A
  • Homomultimer – multiple chains are identical

- Heteromultimer – At least one chain is different

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9
Q

Single amino acid mutations may not have ?

A

A major effect on the overall structure or it can stop the protein from folding

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10
Q

Can the mutation have an impact ? and what is it dependant on ?

A
  • It can have no impact of the protein function or have a massive effect on function
  • It all depends on the mutation and where it is in the protein
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11
Q

What disease is related to a single amino acid change in haemoglobin ?

A

Sickle Cell Anemia

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12
Q

What does a BRAF V600E mutation, activate ?

A

The protein and will transform a cell into a cancer

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13
Q

What are Amino Acids with Electrically Charged Side Chains ?

A

Positive:
R - Arginine
H - Histidine
K - Lysine

Negative:
D - Aspartic Acid
E - Glutamic Acid

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14
Q

What are Amino Acids with Polar Uncharged Side Chains?

A

S - Serine
T - Threonine
N - Asparagine
Q - Glutamine

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15
Q

What are some Amino Acids with Special cases ?

A

C - Cysteine
U - Selenocysteine
G - Glycine
P - Proline

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16
Q

What are Amino Acids with Hydrophobic Side Chain ?

A 
A - Alanine
V - Valine 
I - Isoleucine 
L - Leucine 
M - Methionine 
F - Phenylalanine 
Y - Tyrosine 
W - Tryptophan
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17
Q

Are polypeptide chains flexible ?

A

Polypeptide chains are flexible yet conformationally restricted

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18
Q

Double bond nature of peptide bond cause ?

A

Planar Geometry

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19
Q

What is the angle about the C(alpha)-N bond denoted ?

A

phi (Φ)

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20
Q

What is the angle about the C(alpha)-C bond denoted ?

A

psi (Ψ)

21
Q

Is there free rotations around these angles ?

A

There is Free rotation around Φ and Ψ

22
Q

The entire path of the peptide backbone is known if ?

A

All phi and psi angles are specified

23
Q

What does Ramachandran plots describe ?

A

Describes acceptable Φ/Ψ angles for individual AA’s in a polypeptide chain

24
Q

What does the Ramachandran plots help determine ?

A

Helps determine what types of 2° structure are present

25
Q

Examples of Secondary Structure ?

A
  • Alpha helix
  • Beta strand
  • Coil, loops and turns
26
Q

Explain a little about alpha-helix ?

A
  • First proposed by Linus Pauling and Robert Corey in 1951
  • Identified in keratin by Max Perutz
  • A ubiquitous component of proteins
  • Stabilised by H-bonds
27
Q

How are the H-bonds orientated in the alpha-helix?

A

All H-bonds in the alpha-helix are oriented in the same direction giving the helix a dipole with the N-terminus being positive and the C-terminus being negative

28
Q

What amino acids destabilise alpha-helix ?

A

Glycine and Proline

29
Q

In an amphiphatic alpha helices, what does darker side have ?

A

Mostly hydrophobic AA’s

30
Q

Two amphipathic helices can associate through ?

A

Hydrophobic interactions

31
Q

Explain a little about beta-strands and beta-sheets ?

A
  • Also first postulated by Pauling and Corey, 1951
  • β-strands are extended polypeptide chains
  • A β-sheet consists of two or more side-by-side hydrogen-bonded β strands
  • Strands may be parallel or antiparallel
  • Anti-parallel beta-sheets more stable
32
Q

In beta-sheets, where do the side chains point ?

A

Side chains point alternately above and below the plane of the beta-sheet

33
Q

Beta sheet can be composed of ?

A

2 to 15 beta-strands

34
Q

Each beta strand on average is made of ?

A

6 amino acids

35
Q

Explain what loops contain, where it is found and what it connects ?

A
  • Loops usually contain hydrophilic residues
  • Found on surfaces of proteins
  • Connect alpha-helices and beta-sheets
36
Q

Explain Turns ?

A
  • Loops with < 5 AA’s are called turns
  • Beta-turns are common
  • Different types of turns eg. I, II
37
Q

What do beta-turns allow ?

A

It allows the peptide chain to reverse direction

38
Q

What amino acids are prevalent in beta turns ?

A

Proline and Glycine

39
Q

What are super-secondary structures also known as ?

A

Motifs

e.g. helix-loop-helix, coiled coil, helix bundle and etc

40
Q

What does the tertiary structure of a protein defines?

A

The specific overall 3-D shape of the protein

41
Q

Tertiary structure is based on various types of interactions between ?

A

The side chains of the peptide chain

42
Q

What is formed when motifs combine ?

A

Domains are formed

43
Q

What are Domains ?

A

They independent folding units in a 3° structure of a protein

44
Q

Domains combine to form ?

A

Protein’s tertiary structure

45
Q

How do you assess the similarity between proteins?

A

Sequence-based method:

Sequence Identity (%) = number of identical residues ÷ number of residues aligned x 100

46
Q

Quaternary structure describes?

A
  • The organisation of subunits in a protein with multiple subunits (oligomeric protein)
47
Q

What can quaternary structures have ?

A

Homo-multimers or hetero-multimers

48
Q

In a quaternary structure, how are the subunits held together by ?

A

Non-covalent interactions

49
Q

Oligomeric protein is more stable than ?

A

Disassociated subunits

Structural Basis of Biological Function (9 decks)

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